runHyperKEGG: Run KEGG pathway analysis based on hypergeometric test from a...
In EMA: Easy Microarray Data Analysis

Description Usage Arguments Details Value Author(s) See Also Examples

Run KEGG pathway analysis based on hypergeometric test from a probeset list

1 2	runHyperKEGG(list, pack.annot, categorySize = 1, name = "hyperKEGG", htmlreport = TRUE, txtreport = TRUE, tabResult = FALSE, pvalue = 0.05)

`list`	vector of character with probeset names
`pack.annot`	character string, annotation package to use
`categorySize`	integer, minimum size for category, by default = 1
`name`	character, name for output files, by default "hyperKEGG"
`htmlreport`	logical, if TRUE, a html report is created, by default TRUE
`txtreport`	logical, if TRUE, a txt report is created, by default TRUE
`tabResult`	logical, if TRUE, a list with the results is created, by default FALSE
`pvalue`	numeric, a cutoff for the hypergeometric test pvalue, by default 0.05

runHyperKEGG needs packages GOstats and KEGG.db from Bioconductor.

Txt and html report

Data.frame with KEGG Id, pvalue, Odd Ratio, Expected count, Size and KEGG Term

Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupe

hyperGTest,runHyperGO

## Not run: 
require(hgu133plus2.db)
data(marty)

## Probe list
probeList <- rownames(marty)[1:50]

## Hypergeometric test for KEGG pathway
res <- runHyperKEGG(probeList, htmlreport = FALSE, txtreport = FALSE,
    tabResult = TRUE, pack.annot = "hgu133plus2.db")

## End(Not run)